Leaking chimney/roof

...dealing with a builder whom we have found out the hard way has cut corners on our 5 month old home.
We have now noticed a bad water leak around a brick chimney where it goes through a shingled roof. Last week we had about 4 inches of rail and collected about 2 gallons of water leaking in from all four sides of the chimney/roof juncture. Of course, a single hole in the flashing on one side could be causing water to enter and run all around the 4 sides - can't really tell as wood framing is in the way.
We are uncertain of the exact cause and apropriate fix. The builder's original roofer was already out once, and put some extra roofing caulk (not sure of the actual name) around the top of the flashing. He suggested that the problem might be within the chimney, as the clay flue liner doesn't look like it was mortered well and was slightly offset over the last few flue pieces to move the liner over a few inches to center it. He claimed that wind-blown rain might be entering the chimney flue and traveling through the poor morter joints into the brick outside. I've installed a plastic bag over the chimney/flue opening, however, and the water is still leaking.
Another issue is the quality of the brick work in the attic - instead of a neat brick job, the masons simply slapped whole and broken brick around the flue lining without full morter joints. The thing looks terrible, and not particularly strong, but it is confined with the attic. That is the area where the water is appearing and dripping onto the ceiling. We now know that the builder hired very bad masons, some of whom had little or no experience.
The Question: Is there any way that the poor masonary job could be contributing to the leak, or is the problem most likely due to an incorrect flashing job on the roof? I know that a brick wall is pourous, so I am imagining a scenario where water running down the roof might hit the side of the brick chimney, go right through porous brick and travel down the inside of the chimney until it meets the poor brick/morter job in the attic. Because morter is missing there and some brick is turned sideways etc., the water could then run back outside the brick wall.
The other possibility is that the masonary job in the attic is strictly cosmetic and the problem is confined to the roof flashing. What, however, could a roofer do wrong that would make the leak so severe (2 gallons or more a day)? There is flashing in place and I can't see anything obviously wrong with it.
We have an inspector coming out to look at it soon, but I wanted to get as many opinions about this as possible.
Thanks in advance
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This may sound radical - but the only way you're gonna get the builder to address all of these issues (cosmetic and strutrural) if if somehow the entire chimmny mysteriously "collapsed."
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Any or all of the conditions you mention are possible sources of leaks. Make sure your "inspector" gets up on the roof and looks at flashing and chimney cap; into the attic and looks at the flue and the brick work. If you are not comfortable with his attention to detail or his discussion of the problem, you * may * have to hire a forensic architect or engineer who may have a deeper technical background.
You should have a contract with the General Contractor rather than with his sub contractors. If this is the case, you don't have to struggle with the subs, who can pass the hot potatoe around from one to another until you give up. The GC should have a contract with you and it is his responsilbility to see the problem is fixed. You can use whatever investigative reports to add force to your request that you get a house that meets the standards of the business.
TB
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